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If you use plots from MultiQC in a publication or presentation, please cite:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

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Please remember to cite the tools that you use in your analysis.

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About MultiQC

This report was generated using MultiQC, version 1.26

You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

MultiQC is published in Bioinformatics:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

MultiQC is developed by:

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.

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Report generated on 2025-04-13, 15:07 UTC based on data in: /home/runner/work/pmultiqc/pmultiqc/data

pmultiqc

pmultiqc is a MultiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms, MaxQuant.URL: https://github.com/bigbio/pmultiqc

Experimental Design

This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.

You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html

Showing ⁰/₂ rows and ⁵/₅ columns.

Sample Name	MSstats_Condition	MSstats_BioReplicate	Fraction_Group	Fraction	Label
1	CT=Mixture;CN=UPS1;QY=0.1fmol	1
↳ RD139_Narrow_UPS1_0_1fmol_inj1			1	1	1
↳ RD139_Narrow_UPS1_0_1fmol_inj2			2	1	1
2	CT=Mixture;CN=UPS1;QY=0.25fmol	2
↳ RD139_Narrow_UPS1_0_25fmol_inj1			3	1	1
↳ RD139_Narrow_UPS1_0_25fmol_inj2			4	1	1

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: experimental_design_table

Sort	Column	Description	ID
\|\|	MSstats_Condition	MSstats Condition	`MSstats_Condition`
\|\|	MSstats_BioReplicate	MSstats BioReplicate	`MSstats_BioReplicate`
\|\|	Fraction_Group	Fraction Group	`Fraction_Group`
\|\|	Fraction	Fraction Identifier	`Fraction`
\|\|	Label	Label	`Label`

Summary Table

This table shows the quantms pipeline summary statistics.

Showing ⁰/₁ rows.

#Peptides Quantified	#Proteins Quantified
5729	1605

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: identification_summary_table_table

Sort	Visible	Group	Column	Description	ID	Scale
\|\|			#Proteins Quantified	#Proteins Quantified	`Proteins_Quantified`

Pipeline Result Statistics

This plot shows the quantms pipeline final result.

Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、 and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.

Showing ⁰/₄ rows and ⁷/₇ columns.

Spectra File	Sample Name	Condition	Fraction	#Peptide IDs	#Unambiguous Peptide IDs	#Modified Peptide IDs	#Protein (group) IDs
RD139_Narrow_UPS1_0_1fmol_inj1	1	CT=Mixture;CN=UPS1;QY=0.1fmol	1	5407	5407	871	1552
RD139_Narrow_UPS1_0_1fmol_inj2	1	CT=Mixture;CN=UPS1;QY=0.1fmol	1	5434	5434	880	1562
RD139_Narrow_UPS1_0_25fmol_inj1	2	CT=Mixture;CN=UPS1;QY=0.25fmol	1	5572	5572	901	1578
RD139_Narrow_UPS1_0_25fmol_inj2	2	CT=Mixture;CN=UPS1;QY=0.25fmol	1	5558	5558	896	1588

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: result_statistics_table

Sort	Column	Description	ID
\|\|	Sample Name	Sample identifier	`sample_name`
\|\|	Condition	Combination of possible study variables	`condition`
\|\|	Fraction	Fraction identifier	`fraction`
\|\|	#Peptide IDs	The number of identified PSMs in the pipeline	`peptide_num`
\|\|	#Unambiguous Peptide IDs	The number of unique peptides in the pipeline. Those that match only one protein in the provided database	`unique_peptide_num`
\|\|	#Modified Peptide IDs	Number of modified identified peptides in the pipeline	`modified_peptide_num`
\|\|	#Protein (group) IDs	The number of identified protein(group)s in the pipeline	`protein_num`

Number of Peptides identified Per Protein

This plot shows the number of peptides per protein in quantms pipeline final result

This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.

Created with MultiQC

Peptides Quantification Table

This plot shows the quantification information of peptides in the final result (mainly the mzTab file).

The quantification information of peptides is obtained from the MSstats input file. The table shows the quantitative level and distribution of peptides in different study variables, run and peptiforms. The distribution show all the intensity values in a bar plot above and below the average intensity for all the fractions, runs and peptiforms.

BestSearchScore: It is equal to 1 - min(Q.Value) for DIA datasets. Then it is equal to 1 - min(best_search_engine_score[1]), which is from best_search_engine_score[1] column in mzTab peptide table for DDA datasets.
Average Intensity: Average intensity of each peptide sequence across all conditions with NA=0 or NA ignored.
Peptide intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of fractions, and then mean intensity in technical replicates/biological replicates separately.

Showing ⁰/₅₀ rows and ⁶/₆ columns.

PeptideID	Protein Name	Peptide Sequence	Best Search Score	Average Intensity	CT=Mixture;CN=UPS1;QY=0.1fmol	CT=Mixture;CN=UPS1;QY=0.25fmol
1	TOLA_ECOLI	AAAEADDIFGELSSGK	1.0000	5.9278	5.8889	5.9636
2	G3P2_ECOLI	AAAENIIPHTTGAAK	1.0000	5.8269	5.7804	5.8688
3	RLMH_ECOLI	AAAEQSWSLSALTLPHPLVR	1.0000	6.2390	6.1953	6.2787
4	PDXJ_ECOLI	AAAEVGAPFIEIHTGCYADAK	0.9997	5.4008	5.4976	5.2760
5	RL10_ECOLI	AAAFEGELIPASQIDR	1.0000	8.2489	8.2045	8.2892
6	YFGM_ECOLI	AAAQLQQGLADTSDENLK	1.0000	6.3880	6.3969	6.3789
7	YFGM_ECOLI	AAAQLQQGLADTSDENLKAVINLR	1.0000	6.1712	6.0321	6.2764
8	RHLE_ECOLI	AAATGEALSLVCVDEHK	1.0000	5.7073	5.6799	5.7331
9	SYP_ECOLI	AAATQEMTLVDTPNAK	1.0000	6.2840	6.2035	6.3518
10	EUTL_ECOLI	AACNAFTDAVLEIAR	1.0000	5.6299	5.6044	5.6541
11	ACRB_ECOLI	AADGQMVPFSAFSSSR	1.0000	6.0764	5.9387	6.1808
12	YIDA_ECOLI	AADGSTVAQTALSYDDYR	0.9998	5.6988	5.6826	5.7144
13	ADHE_ECOLI	AADIVLQAAIAAGAPK	1.0000	7.3764	7.3461	7.4048
14	NARG_ECOLI	AADLVDALGQENNPEWK	1.0000	5.6929	5.6454	5.7357
15	DNAK_ECOLI	AADNKSLGQFNLDGINPAPR	0.9998	5.5334	5.4957	5.5510
16	OXYR_ECOLI	AADSCHVSQPTLSGQIR	1.0000	6.2817	6.2485	6.3126
17	TALA_ECOLI	AAEELEKEGINCNLTLLFSFAQAR	1.0000	6.2640	6.2059	6.3153
18	HEMY_ECOLI	AAELAGNDTIPVEITR	0.9999	6.4392	6.4256	6.4523
19	SYL_ECOLI	AAENNPELAAFIDECR	1.0000	6.6836	6.6402	6.7231
20	TALB_ECOLI	AAEQLEKEGINCNLTLLFSFAQAR	1.0000	6.9806	6.8963	7.0512
21	MBHM_ECOLI	AAESALNIDVPVNAQYIR	1.0000	6.1335	6.1304	6.1366
22	DNAG_ECOLI	AAESGVSRPVPQLKR	0.9999	5.1143	4.9585	5.2288
23	HDFR_ECOLI	AAESLYLTQSAVSFR	1.0000	5.7540	5.7105	5.7935
24	RNE_ECOLI	AAESRPAPFLIHQESNVIVR	1.0000	6.5752	6.5572	6.5925
25	HFLK_ECOLI	AAFDDAIAARENEQQYIR	1.0000	5.8013	5.6354	5.9210
26	AROF_ECOLI	AAFPLSLQQEAQIADSR	1.0000	5.9273	5.9306	5.9241
27	AROF_ECOLI	AAFPLSLQQEAQIADSRK	0.9998	5.7612	5.7318	5.7887
28	BOLA_ECOLI	AAFQPVFLEVVDESYR	1.0000	6.4279	6.4107	6.4444
29	CLPB_ECOLI	AAGATTANITQAIEQMR	1.0000	5.9836	5.9726	5.9908
30	YBIS_ECOLI	AAGEPLPAVVPAGPDNPMGLYALYIGR	1.0000	5.9628	5.8381	6.0596
31	SDHA_ECOLI	AAGLHLQESIAEQGALR	1.0000	5.4225	5.4295	5.4154
32	TALA_ECOLI	AAGLSQYEHLIDDAIAWGK	0.9998	5.1833	5.1162	5.2413
33	TALA_ECOLI	AAGLSQYEHLIDDAIAWGKK	1.0000	5.8222	5.7763	5.8638
34	ADHE_ECOLI	AAGVETEVFFEVEADPTLSIVR	1.0000	6.4683	6.5168	6.4137
35	ADHE_ECOLI	AAGVETEVFFEVEADPTLSIVRK	0.9998	6.8321	6.7758	6.8819
36	ENO_ECOLI	AAGYELGKDITLAMDCAASEFYK	1.0000	6.6467	6.6291	6.6636
37	YEBE_ECOLI	AAHQDEPQFGAQSTPLDER	0.9998	5.6491	5.6220	5.6746
38	RIBB_ECOLI	AAIADGAKPSDLNRPGHVFPLR	1.0000	6.4630	6.4313	6.4926
39	DEOC_ECOLI	AAIAYGADEVDVVFPYR	1.0000	6.7499	6.6917	6.8012
40	IDH_ECOLI	AAIEYAIANDRDSVTLVHK	1.0000	6.2872	6.2689	6.3048
41	DPO1_ECOLI	AAINAPMQGTAADIIKR	0.9998	5.8750	5.8517	5.8972
42	SYFA_ECOLI	AAISQASDVAALDNVR	1.0000	6.5821	6.5777	6.5864
43	SYFA_ECOLI	AAISQASDVAALDNVRVEYLGK	1.0000	6.0451	5.9836	6.0990
44	MUKF_ECOLI	AAISSCELLLSETSGTLR	0.9998	5.4539	5.3950	5.5057
45	MSCM_ECOLI	AAKPAQPEVVEALQSALNALEER	0.9999	5.2647	5.1693	5.3428
46	AMPN_ECOLI	AALEQLKGLENLSGDLYEK	1.0000	6.2583	6.1947	6.3138
47	DBHA_ECOLI	AALESTLAAITESLK	1.0000	7.0020	7.0119	6.9919
48	HEM3_ECOLI	AALPPEISLPAVGQGAVGIECR	0.9999	6.3107	6.2797	6.3396
49	SDHA_ECOLI	AALQISQSGQTCALLSK	0.9999	5.5633	5.4781	5.6344
50	DHE4_ECOLI	AANAGGVATSGLEMAQNAAR	1.0000	5.7321	5.6606	5.7934

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: quantification_of_peptides_table

Sort	Column	Description	ID
\|\|	Protein Name	Name/Identifier(s) of the protein (group)	`ProteinName`
\|\|	Peptide Sequence	Peptide Sequence	`PeptideSequence`
\|\|	Best Search Score	Best Search Score	`BestSearchScore`
\|\|	Average Intensity	Average intensity across all conditions	`Average_Intensity`
\|\|	CT=Mixture;CN=UPS1;QY=0.1fmol	CT=Mixture;CN=UPS1;QY=0.1fmol	`CT_Mixture_CN_UPS1_QY_0_1fmol`
\|\|	CT=Mixture;CN=UPS1;QY=0.25fmol	CT=Mixture;CN=UPS1;QY=0.25fmol	`CT_Mixture_CN_UPS1_QY_0_25fmol`

Protein Quantification Table

This plot shows the quantification information of proteins in the final result (mainly the mzTab file).

The quantification information of proteins is obtained from the msstats input file. The table shows the quantitative level and distribution of proteins in different study variables and run.

Peptides_Number: The number of peptides for each protein.
Average Intensity: Average intensity of each protein across all conditions with NA=0 or NA ignored.
Protein intensity in each condition (Eg. CT=Mixture;CN=UPS1;QY=0.1fmol): Summarize intensity of peptides.

Showing ⁰/₅₀ rows and ⁵/₅ columns.

ProteinID	Protein Name	Number of Peptides	Average Intensity	CT=Mixture;CN=UPS1;QY=0.1fmol	CT=Mixture;CN=UPS1;QY=0.25fmol
1	3PASE_ECOLI	1	5.6235	5.6046	5.6415
2	5DNU_ECOLI	1	5.1934	5.1118	5.2621
3	6PGD_ECOLI	10	7.4306	7.4143	7.4446
4	6PGL_ECOLI	2	6.5057	6.4721	6.5331
5	AAEB_ECOLI	1	6.1800	6.1410	6.2158
6	AAS_ECOLI	4	6.0912	6.0728	6.0645
7	AAT_ECOLI	2	7.1735	7.1515	7.1944
8	ABGT_ECOLI	1	5.2444	5.3301	5.1374
9	ACCA_ECOLI	10	7.5188	7.4724	7.5607
10	ACCC_ECOLI	11	7.5447	7.5080	7.5786
11	ACCD_ECOLI	4	6.9568	6.9438	6.9695
12	ACEA_ECOLI	10	7.0495	7.0004	7.0936
13	ACFD_ECOLI	8	6.8296	6.7905	6.8657
14	ACKA_ECOLI	9	8.1525	8.1204	8.1816
15	ACNA_ECOLI	5	6.1236	6.0315	6.1795
16	ACNB_ECOLI	11	7.4528	7.4149	7.4828
17	ACRA_ECOLI	6	7.4974	7.4509	7.5394
18	ACRB_ECOLI	6	6.7660	6.6959	6.8263
19	ACSA_ECOLI	2	5.6039	5.6355	5.5511
20	ACUI_ECOLI	5	7.0524	6.9583	7.1097
21	ACYP_ECOLI	1	5.6173	5.6039	5.6238
22	ADD_ECOLI	5	7.1199	7.1375	7.1068
23	ADEC_ECOLI	1	5.3880	5.3527	5.4207
24	ADHE_ECOLI	33	8.5391	8.4942	8.5798
25	ADHP_ECOLI	2	5.8313	5.8293	5.8333
26	ADIA_ECOLI	3	5.9251	5.8502	5.9848
27	ADPP_ECOLI	2	6.3923	6.3622	6.4204
28	AGP_ECOLI	3	6.1377	6.1064	6.1668
29	AHPC_ECOLI	9	7.9186	7.8892	7.9463
30	AHPF_ECOLI	9	7.4292	7.4037	7.4533
31	AHR_ECOLI	1	5.0382	5.1352	4.9801
32	AK1H_ECOLI	7	6.4884	6.4593	6.5158
33	AK2H_ECOLI	4	6.5019	6.4721	6.5298
34	AK3_ECOLI	5	6.6134	6.5366	6.6421
35	ALAA_ECOLI	3	6.6067	6.5814	6.6305
36	ALAC_ECOLI	5	6.4739	6.4394	6.5059
37	ALDB_ECOLI	1	6.0428	6.0105	6.0729
38	ALF1_ECOLI	2	5.7993	5.0883	5.8061
39	ALF_ECOLI	10	7.9717	7.9422	7.9992
40	ALKH_ECOLI	3	6.6459	6.5686	6.7115
41	ALR1_ECOLI	3	6.6652	6.6304	6.6974
42	AMIA_ECOLI	1	5.8082	5.7658	5.8469
43	AMIB_ECOLI	2	5.7290	5.6933	5.7621
44	AMIC_ECOLI	5	5.9764	5.8423	6.0306
45	AMID_ECOLI	1	4.6107	4.3583	4.6972
46	AMN_ECOLI	8	6.7648	6.7423	6.7877
47	AMPA_ECOLI	7	7.1145	7.0752	7.1505
48	AMPC_ECOLI	2	6.1201	6.0621	6.1713
49	AMPH_ECOLI	2	6.1563	6.0922	6.2121
50	AMPN_ECOLI	7	7.0764	7.0526	7.0991

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: quantification_of_protein_table

Sort	Column	Description	ID
\|\|	Protein Name	Name/Identifier(s) of the protein (group)	`ProteinName`
\|\|	Number of Peptides	Number of peptides per proteins	`Peptides_Number`
\|\|	Average Intensity	Average intensity across all conditions	`Average_Intensity`
\|\|	CT=Mixture;CN=UPS1;QY=0.1fmol	CT=Mixture;CN=UPS1;QY=0.1fmol	`CT_Mixture_CN_UPS1_QY_0_1fmol`
\|\|	CT=Mixture;CN=UPS1;QY=0.25fmol	CT=Mixture;CN=UPS1;QY=0.25fmol	`CT_Mixture_CN_UPS1_QY_0_25fmol`

nf-core/quantms Software Versions

nf-core/quantms Software Versions are collected at run time from the software output.URL: https://github.com/nf-core/quantms

Process Name	Software	Version
`ASSEMBLE_EMPIRICAL_LIBRARY`	`DIA-NN`	`1.8.1`
`CUSTOM_DUMPSOFTWAREVERSIONS`	`python`	`3.9.5`
	`yaml`	`5.4.1`
`DIANNCFG`	`sdrf-pipelines`	`0.0.21`
`DIANNCONVERT`	`sdrf-pipelines`	`0.0.21`
`DIANNSUMMARY`	`DIA-NN`	`1.8.1`
`DIANN_PRELIMINARY_ANALYSIS`	`DIA-NN`	`1.8.1`
`INDIVIDUAL_FINAL_ANALYSIS`	`DIA-NN`	`1.8.1`
`MSSTATS`	`bioconductor-msstats`	`4.2.0`
	`r-base`	`4.1.2`
`SAMPLESHEET_CHECK`	`sdrf-pipelines`	`0.0.21`
`SDRFPARSING`	`sdrf-pipelines`	`0.0.21`
`THERMORAWFILEPARSER`	`ThermoRawFileParser`	`1.3.4`
`Workflow`	`Nextflow`	`21.10.6`
	`nf-core/quantms`	`1.1dev`

nf-core/quantms Workflow Summary

- this information is collected when the pipeline is started.URL: https://github.com/nf-core/quantms

Core Nextflow options

runName: voluminous_thompson
containerEngine: docker
launchDir: /home/chengxin/newPR/quantms
workDir: /home/chengxin/newPR/quantms/work
projectDir: /home/chengxin/newPR/quantms
userName: chengxin
profile: test_dia,docker
configFiles: /home/chengxin/newPR/quantms/nextflow.config

Input/output options

input: /home/chengxin/diatestdata/PXD026600/PXD026600Partial2.sdrf.tsv
outdir: ./results_dia

Protein database

database: /home/chengxin/diatestdata/PXD026600/REF_EColi_K12_UPS1_combined.fasta

Database search

allowed_missed_cleavages: 1
instrument: N/A
max_precursor_charge: 3
min_peptide_length: 15
max_peptide_length: 30
max_mods: 2

Modification localization

luciphor_debug: N/A

PSM re-scoring (general)

run_fdr_cutoff: 0.10

PSM re-scoring (Percolator)

description_correct_features: N/A

Consensus ID

consensusid_considered_top_hits: N/A
min_consensus_support: N/A

Isobaric analyzer

select_activation: HCD

Protein Quantification (DDA)

ratios: N/A
normalize: N/A
fix_peptides: N/A

DIA-NN

acquisition_method: N/A
mass_acc_ms2: 13
mass_acc_ms1: 7
scan_window: 8
min_pr_mz: 350
max_pr_mz: 950
min_fr_mz: 500
max_fr_mz: 1500
diann_normalize: N/A

Statistical post-processing

contrasts: pairwise

Quality control

enable_pmultiqc: true

Institutional config options

config_profile_name: Test profile for DIA
config_profile_description: Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.

Max job request options

max_cpus: 2
max_memory: 6 GB
max_time: 2d

Generic options

hostnames: N/A

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pipeline result statistics: Columns

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quantification information of peptides: Columns

Protein Quantification Table Help

quantification information of protein: Columns

nf-core/quantms Software Versions

nf-core/quantms Workflow Summary

v1.26

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Experimental Design

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